Find_primer_sequence_and_reverse_complement_read_within_amplicon.fastq script needed

[kliere]

Hi,

I have a fastq file with merged amplicon sequence reads post Illumina sequencing. However, the library was build by ligating the Illumina adapters to the amplicon. Therefore, the merged amplicon sequences have no common direction. Now I had the idea to use a script that finds the exact sequence of a certain primer and reverse complements those sequence reads within the fastq file. One _is_ able to do this in Geneious, however, I'd rather like to use a script/tool to incorporate into the pipeline I want to establish.
I already looked into BBtools and others, however, couldn't find a tool doing this.

Thank you for any input.

Cheers,

Karsten

[GenoMax]

For reference cross-posted: https://www.biostars.org/p/292377/

Copying my comment there below.

Just that part of the sequence or the whole sequence? If whole sequence is fine then you should be able to select matching reads that contain the sequence you are interested in using bbduk.sh and then you can reverse-complement them using reformat.sh.